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PDBsum entry 2rc9

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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
2rc9
Jmol
Contents
Protein chains
287 a.a. *
Ligands
1AC ×2
Waters ×513
* Residue conservation analysis
PDB id:
2rc9
Name: Membrane protein
Title: Crystal structure of the nr3a ligand binding core complex wi 1.96 angstrom resolution
Structure: Glutamate [nmda] receptor subunit 3a. Chain: a, b. Fragment: unp residues 511-660, 776-915. Synonym: n-methyl-d-aspartate receptor subtype 3a, nr3a, nm nmdar-l1, n-methyl-d-aspartate receptor, chi-1. Engineered: yes
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: grin3a. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: peptides corresponding to n511-r660 and e776 were coupled by a gt dipeptide synthetic linker
Resolution:
1.96Å     R-factor:   0.159     R-free:   0.211
Authors: Y.Yao,M.L.Mayer
Key ref: Y.Yao et al. (2008). Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. EMBO J, 27, 2158-2170. PubMed id: 18636091 DOI: 10.1038/emboj.2008.140
Date:
19-Sep-07     Release date:   05-Aug-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9R1M7  (NMD3A_RAT) -  Glutamate receptor ionotropic, NMDA 3A
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1135 a.a.
287 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transport   1 term 
  Biochemical function     transporter activity     3 terms  

 

 
DOI no: 10.1038/emboj.2008.140 EMBO J 27:2158-2170 (2008)
PubMed id: 18636091  
 
 
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.
Y.Yao, C.B.Harrison, P.L.Freddolino, K.Schulten, M.L.Mayer.
 
  ABSTRACT  
 
NR3 subtype glutamate receptors have a unique developmental expression profile, but are the least well-characterized members of the NMDA receptor gene family, which have key roles in synaptic plasticity and brain development. Using ligand binding assays, crystallographic analysis, and all atom MD simulations, we investigate mechanisms underlying the binding by NR3A and NR3B of glycine and D-serine, which are candidate neurotransmitters for NMDA receptors containing NR3 subunits. The ligand binding domains of both NR3 subunits adopt a similar extent of domain closure as found in the corresponding NR1 complexes, but have a unique loop 1 structure distinct from that in all other glutamate receptor ion channels. Within their ligand binding pockets, NR3A and NR3B have strikingly different hydrogen bonding networks and solvent structures from those found in NR1, and fail to undergo a conformational rearrangement observed in NR1 upon binding the partial agonist ACPC. MD simulations revealed numerous interdomain contacts, which stabilize the agonist-bound closed-cleft conformation, and a novel twisting motion for the loop 1 helix that is unique in NR3 subunits.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20621105 D.Stroebel, S.Carvalho, and P.Paoletti (2011).
Functional evidence for a twisted conformation of the NMDA receptor GluN2A subunit N-terminal domain.
  Neuropharmacology, 60, 151-158.  
20558186 G.M.Alushin, D.Jane, and M.L.Mayer (2011).
Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
  Neuropharmacology, 60, 126-134.
PDB codes: 2qs1 2qs2 2qs4
  21522138 K.M.Vance, N.Simorowski, S.F.Traynelis, and H.Furukawa (2011).
Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.
  Nat Commun, 2, 294.
PDB codes: 3oek 3oel 3oem 3oen
21349697 M.L.Mayer (2011).
Structure and mechanism of glutamate receptor ion channel assembly, activation and modulation.
  Curr Opin Neurobiol, 21, 283-290.  
  21395862 P.Paoletti (2011).
Molecular basis of NMDA receptor functional diversity.
  Eur J Neurosci, 33, 1351-1365.  
21460832 W.Kakegawa, Y.Miyoshi, K.Hamase, S.Matsuda, K.Matsuda, K.Kohda, K.Emi, J.Motohashi, R.Konno, K.Zaitsu, and M.Yuzaki (2011).
D-serine regulates cerebellar LTD and motor coordination through the δ2 glutamate receptor.
  Nat Neurosci, 14, 603-611.  
20097255 M.A.Henson, A.C.Roberts, I.Pérez-Otaño, and B.D.Philpot (2010).
Influence of the NR3A subunit on NMDA receptor functions.
  Prog Neurobiol, 91, 23-37.  
19946266 A.I.Sobolevsky, M.P.Rosconi, and E.Gouaux (2009).
X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor.
  Nature, 462, 745-756.
PDB codes: 3kg2 3kgc
19617541 C.Chaudhry, A.J.Plested, P.Schuck, and M.L.Mayer (2009).
Energetics of glutamate receptor ligand binding domain dimer assembly are modulated by allosteric ions.
  Proc Natl Acad Sci U S A, 106, 12329-12334.  
19910922 E.Karakas, N.Simorowski, and H.Furukawa (2009).
Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit.
  EMBO J, 28, 3910-3920.
PDB codes: 3jpw 3jpy
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.